Bonobos are a species within a species.

Ask any biologist who our closest relative is, and they'll almost certainly say the chimpanzee. However, there is another species of great ape, the bonobo, that we're just as closely related to. This lack of recognition may have something to do with the fact that bonobos only exist as a relatively small population within an isolated pocket of the Congo and were the last of the great apes to be discovered. Or it may be because bonobos have a habit that would probably make them a nightmare for anyone involved in public relations at a place like a zoo: they tend to defuse conflicts by having sex, often with members of the same sex.

And primates in the wild have a lot of situations that can potentially create conflicts. At this year's meeting of the American Association for the Advancement of Science, primatologist Frans de Waal showed how, after having a load of food delivered, a group of bonobos quickly split up into couples and started having sex (including one male that kept on eating while coupling).

It's hard to imagine a sharper contrast with the aggressive, territorial chimpanzees. Yet bonobos and chimps shared a common ancestor less than two million years ago. And, now that we've sequenced the bonobo genome, we've confirmed something that earlier studies have hinted at: from the DNA perspective, we'd have never recognized bonobos as a separate species if we hadn't seen the behavioral differences.

Chimps live in a diverse range of habitats across Africa, and many of these populations have diverged substantially since they branched off from the lineage that eventually gave rise to humans. That means that, as we've sampled chimps from multiple regions across Africa, we've found that there's a lot of diversity on the DNA level.

Bonobos split off from a single one of these populations less than two million years ago and haven't had as much time to diversify. As a result, at the DNA level, every bonobo falls within the normal variability of the chimpanzees—from this perspective, they look just like a sub-population of chimps. (They look a fair bit like them physically as well, leaving the behavioral differences as the easiest way of telling the species apart.)

The genome indicates that the split between bonobos and chimps was in the area of 1 million-2 million years ago, consistent with the proposal that the formation of the Congo river basin left the Bonobos geographically isolated from other populations of chimps.

Based on the differences between the two chromosomes, all bonobos are likely to be 99.9 percent identical at the DNA level; they differ from the typical chimp only by 0.4 percent, and are 98.7 percent similar to humans.

The species have also preserved different sequences that they shared with our common ancestor. About 1.6 percent of the human genome is more closely related to bonobos than chimps, while 1.7 percent is more closely related to the chimp versions of the sequence. Overall, the completion of this sequence provides us a slightly better picture of what the genome of our common ancestor was likely to look like.

But really, the key finding here is the confirmation that the variation within the bonobo genome places them squarely within the normal variability of chimps. There's been a bit of a tendency to assume that as long as there's enough differences on the DNA level, we're looking at different species. The converse of that, of course, would mean that any populations that are sufficiently similar must be the same species—an idea that doesn't seem to work here.

The strong behavioral differences between chimps and bonobos, as well as the relatively recent split between them, may provide us with some information on the sorts of genetic changes that drive complex behaviors. And, as the authors suggest, bringing humans into the analysis might tell us something about the behaviors of the last common ancestor of the three species, which the paper argues was probably a mosaic of traits retained by its three living descendants.